Search

Deze studie gaat in op interacties tussen elementen als K, Mg, Ca, N, Cl en in hoeverre deze van invloed zijn op de opbrengst en kwaliteit van akkerbouwgewassen. De werkingsmechanismen worden toegelicht. Voor belangrijke akkerbouwgewassen als aardappel en suikerbieten wordt nagegaan hoe deze onder Nederlandse omstandigheden kunnen uitwerken en of dit gevolgen dient te hebben voor de bemestingsadvisering. De gangbare bemestingsadvisering is gebaseerd op het uitgangspunt dat er een minimum hoeveelheid van een nutriënt beschikbaar moet zijn in de bodem voor een goede opbrengst. Daarnaast is er een alternatieve benadering waarbij nutriënten als K, Mg, Ca in een vaste verhouding in de bodem aanwezig moeten zijn. Hier wordt nader op ingegaan.

A more rapid increase in night-time temperature compared with day-time temperature and the increased frequency of heat waves associated with climate change present a serious threat to rice (Oryza sativa L.) production and food security. This thesis aims to understand the impact of high night-time temperature (HNT) and high day-time temperature (HDT) on rice grain yield and grain quality and to examine adaptation strategies to cope with high-temperature stresses. Grain yield and quality of a susceptible indica genotype (Gharib) and all tested hybrids, when exposed to HNT in the field, were significantly reduced across seasons, with less average reduction in the dry season than in the wet season, indicating that other environmental factors under field conditions may contribute to impacts of HNT on yield. Among the different yield components, a reduced number of spikelets m−2 significantly contributed to yield loss under HNT followed by the consistently lower single-grain weight across all genotypes, while the impact of the decrease in percentage seed-set was less and season-specific. Lower grain yield and poorer grain quality in susceptible cultivar Gharib were associated with a significant reduction in non-structural carbohydrate translocation after flowering, resulting in reduced grain-filling duration. Increased total nitrogen application did not alleviate the negative impact of HNT. The proposed model approach showed that there were significant differences among cultivars in their changes in source-sink relationships in response to HNT. Given that rice grain yield and quality are challenged by a rise in HDT and HNT, in particular at flowering and during grain filling, differential impacts of HNT and HDT during these critical stages were observed. For the single-grain growth during grain filling, HDT either independently or in combination with HNT exerted greater influences than HNT on the grain filling dynamics, activities of starch metabolism enzymes, temporal starch accumulation patterns, and the process of chalk formation. During flowering, HDT increased spikelet sterility in tested hybrids and hybrids were less tolerant to high temperatures than high-yielding inbred varieties. Moreover, in contrast with HNT, HDT played a dominant role in determining spikelet fertility. Novel observations with a series of snapshots of dynamic fertilization processes demonstrated that disturbances in the pre-fertilization phase were the primary causes for heat-induced spikelet sterility, indicating the effectiveness of employing the early-morning flowering trait for mitigating the impact of heat stress at flowering on rice.

Achtergrondverlaging is dat deel van de gemeten grondwaterstandsdaling, dat niet door hydrologische berekeningen wordt verklaard. In het Nederlandse zandlandschap bedraagt dit deel, gemeten vanaf de jaren vijftig van de vorige eeuw, gemiddeld enkele decimeters. In dit artikel laten we zien dat de achtergrondverlaging in de provincie Noord-Brabant waarschijnlijk grotendeels is veroorzaakt door de afname van de grondwateraanvulling. Die afname hangt samen met veranderingen in het landgebruik en met een stijging van gewasopbrengsten in de landbouw.

Jatropha curcas L. is a biofuel crop that has not lived up to expectations due to a combination of hype and disappointment and biophysical factors. This PhD thesis is based on the plant production component of the JARAK programme which aimed to bridge the gap between truth and fiction. This study reviewed the jatropha hype and disappointment and further investigated the hypothesis that jatropha growth and yield are limited by biophysical factors of plant characteristics, cropping systems, and management. My review of the hype and disappointment shows that despite the high expectations fuelled by market pull and technology push, and numerous actors, the commercial potential for jatropha is limited by policy and governance, economics, social, technology, logistical, and environmental. A study of the biophysical components confirms that no current varieties suited to different cropping systems and locations are available. Jatropha aboveground biomass is partitioned predominantly into a structure of stem, branches, and twigs. The below to aboveground biomass ratio was 0.5 and fruit which was found only on productive twigs accounted for the smallest portion of biomass measured. Seed yields were disappointingly small (109 kg ha-1) and were largest in monoculture, followed by intercropping and hedgerows in that order, although yields were influenced by age and management of pruning and fertiliser. Seed yield across the three cropping systems can be predicted using plant height and the number of productive twig/branch, although the number of inflorescence clusters per productive twig may be important. Intercropping between jatropha and maize (Zea mays L.) resulted in competition for resources both belowground and aboveground that reduced maize yields. Shoot pruning was effective in managing aboveground competition, while root pruning and root barriers effectively managed competition belowground. Leaf prunings provided a limited, but positive fertility effect on maize yield comparable to 21 kg N ha-1. Jatropha - maize intercropping has potential for long-term productivity provided management practices such as fertiliser, pruning, and planting density can be developed to minimise competition and enhance complementarity. Based on my review of the jatropha hype and disappointment and my biophysical research results, the planting of jatropha by smallholders, or as a plantation crop cannot be recommended. Once the issues I highlight have been resolved and market confidence restored, jatropha may finally become a commercial source of biodiesel able to provide improved socio-economic and environmental benefits.

Intercropping is the cultivation of two or more crop species simultaneously in the same field, while relay intercropping means that the growing periods of the crop species are only partially overlapping. Intercropping has advantages with respect to productivity, resource capture, build-up of soil organic matter, and pest and disease suppression. This thesis aims to quantify and explain the yield advantages in wheat-maize relay intercropping and to assess the importance of intercropping for food production and land use efficiency. Wheat-maize intercropping had land equivalent ratios around or above one in two experiments in the Netherlands. Wheat in border rows showed major yield increases, and this yield increase was due to increases in the number of tillers per plant and the number of kernels per ear. The yield advantage of intercropped wheat was associated with a high radiation interception and radiation use efficiency (RUE). Under Dutch growing conditions, maize performance in the intercrop was constrained. Intercropping had a negative effect on the yield per plant and radiation use efficiency of maize. A strip intercrop model was developed, parameterized and tested with data on wheat-maize intercropping in the Netherlands. The model simulates radiation interception and growth in relay-strip intercrops with two species in different planting configurations. The model also allows simulating the consequences of border row effects for total system productivity. Bayesian analysis was applied to calibrate radiation use efficiency of wheat and maize in sole crops and intercrop. Intercropped wheat had higher a RUE than sole wheat, while intercropped maize had a lower RUE than sole maize. Intercropped maize had less favourable leaf traits (e.g. nitrogen content) during the flowering stage than sole maize in 2014, but the leaves in the intercrop had a higher photosynthetic rate than those in the sole crop. Possible explanations for this finding include differences between sole and mixed crops in water acquisition from soil, light distribution in the canopy, nitrogen distribution within the leaf and the contribution of the ear leaf to the growth of the cob. The low radiation use efficiency in intercropped maize may relate to nitrogen deficiency during grain filling. New concepts for potential yield, yield gain and yield gap in intercropping were developed in this thesis. Using crop model simulations and farm survey data, those concepts were operationalized in the context of wheat and maize production in an oasis area (Zhangye city) in northwest China. Wheat-maize intercropping resulted in substantial yield gains under potential and actual growing conditions. A comparison of potential and actual yields indicated a yield gap of 33% for sole wheat, 49% for sole maize, 15% for intercropped wheat, and 51% for intercropped maize. The land use analysis showed that discontinuing the use of intercropping in this region will decrease grain production substantially. Overall, this thesis studied the growth and productivity of wheat-maize intercropping at organ, plant and cropping system level, and also assessed its contribution to grain production at a regional level. The findings suggest that intercropping of food crops provides opportunities to meet increasing food demands. New technologies are needed to make strip intercropping efficient in terms of labour use and breeding should pay attention to cultivars that are suitable for intercropping.

Global livestock production is expected to increase in future decades, and expansion of the agricultural area for feed production is not desired. Hence, increasing livestock production per unit agricultural area is essential. The bio-physical scope to increase production of livestock systems with the corresponding feed crop production (feed-crop livestock systems) could not be assessed generically at the start of this research. In crop production, however, crop models based on concepts of production ecology are widely applied to assess the bio-physical scope to increase actual production. The difference between the biophysical scope and actual production is referred to as the yield gap. The objectives of this thesis were 1) to develop a generic framework to assess the scope to increase production in feed crop-livestock systems based on concepts of production ecology, 2) to develop a generic livestock model simulating potential (i.e. maximum theoretical) and feed-limited livestock production, and 3) to apply this framework and model to feed-crop livestock systems, and conduct yield gap analyses. Concepts of production ecology for livestock were specified in more detail. Feed efficiency at herd level was a suited benchmark for livestock production only, and production of animal-source food per hectare for feed-crop livestock systems. Application of the framework showed that the yield gap was 79% of the potential beef production of a cow-calf system, and 72% of a cow-calf-fattener system in the Charolais region of France. The model LiGAPS-Beef (Livestock simulator for Generic analysis of Animal Production Systems – Beef cattle) was developed to simulate potential and feed-limited production of beef cattle using input data about animals’ genotype, climate, and feed quality and availability. The model consists of sub-models describing thermoregulation, feed intake and digestion, and energy and protein utilisation. Model evaluation under different agro-ecological conditions indicated live weight gain was estimated fairly well (15.4% deviation from measured values). LiGAPS-Beef was coupled with crop growth models to simulate potential and resource-limited production of twelve grass-based beef production systems in the Charolais region. Resource-limited production combines feed-limited production of cattle and water-limited production of feed crops. Yield gaps were on average 85% of potential live weight production per hectare, and 47% of resource-limited production. Yield gaps were attributed to feed quality and quantity limitation (41% of potential production), water-limitation in feed crops (31%), the combination of sub-optimal selling or slaughter weights, culling rates, calving dates, age at first calving, and stocking densities (9%), and the combination of prolonged calving intervals and calf mortality (2%). Improved grassland management and an earlier start of the grazing season may increase live weight production per hectare. Furthermore, the resource-limited production of bulls was simulated to increase by 6-14% from 1999-2006 up to 2050 due to climate change. From the results of this thesis, it can be concluded that 1) a generic framework using concepts of production ecology is available now to assess the bio-physical scope to increase production in feed-crop livestock systems per unit area; 2) the mechanistic model LiGAPS-Beef simulates potential and feed-limited production of beef cattle fairly well; 3) combining LiGAPS-Beef with crop growth models allows to quantify yield gaps in feed-crop livestock systems, and to analyse these yield gaps. The method described in this thesis can be used subsequently to identify options to mitigate yield gaps, and to increase livestock production per unit area, which may contribute to sustainable intensification of agriculture.

Tomato (Solanum lycopersicum L.) is a vegetable crop with high potential to contribute to poverty reduction via increased income and food security. It is widely grown by smallholders, has high productivity and its demand is increasing. Ethiopia produced about 30,700 Mg of tomatoes on 5,027 ha annually in 2014/2015. Average yields are only 6.1 Mg ha-1, below the world average yields. There is both a need and a potential to increase tomato production per unit area. The aim of this thesis is to analyze the irrigated tomato production systems of smallholder farmers in Ethiopia, to survey and characterize the tomato in selected ecoregions and seasons, and to identify yield-limiting or yield-reducing factors and opportunities to enhance yield by using a combination of surveys and field experiments. Field experiments on optimization of yield and quality of field-grown tomato were carried out at Ziway, Ethiopia, for two seasons to study the impact of different irrigation practices applied, based on local empirical practices, deficit irrigation, or crop water requirement. This thesis begins with a survey of tomato production systems. The survey details the area and production in various zones and for each of these zones yield- determining, yield-limiting, and yield-reducing factors and opportunities for improving yield and quality are indicated. It also avails area, production and yield data for each growing season and typifies the production systems in these zones. Low temperature (cold) from October-January and shortage of improved seeds are recognized as yield-determining factors, whereas insufficient water and nutrient (fertilizer) supply proved to be yield-limiting factors across zones. Late blight (Phytophthora infestans), Fusarium wilt (Fusarium oxysporum) and different pests and weeds are identified as yield-reducing factors in the zones. Experienced growers who have access to extension service recorded significant yield increment. Farmers Research Groups improved actual average yield with the use of improved technology (improved varieties and quality seed), and better efficiencies of water and fertilizer use. This study quantified influences of irrigation systems and strategies on growth-determining tomato features. Variation in irrigation systems and strategies accounted for variation in growth and dry matter accumulation. Greater performance for yield-related traits was obtained with drip irrigation based on crop water requirement for tomato varieties. Examination of plants showed also that local empirical irrigation is responsible for the occurrence of Phytophthora root rot, whereas deficit irrigation proved cause for occurrence of Fusarium wilt (Fusarium oxysporum), blossom end rot and broome rape (Orobanche ramosa) on roots or leaves, stems or fruits. The experiments on irrigation scheduling with different irrigation systems and strategies gave useful indications on the possibility to improve commercial yield (CY) and water use efficiency. Promising results on CY and agronomical water use efficiency of tomato were achieved with drip irrigation based on crop water requirement, while for the biological water use efficiency higher value was obtained with deficit drip irrigation in both seasons. The findings indicate that the CY was decreased significantly for deficit by 50% in drip irrigation and deficit by 50% in furrow irrigation in both seasons. Mean CY for drip irrigation according to crop water requirement increased by 51% and 56% compared with deficit drip irrigation, whereas furrow irrigation based on crop water requirement increased by 52% and 54% compared with deficit furrow in Experiments 1 and 2, respectively. However, water use efficiency decreased with the increasing water volume. Simultaneous measurements of rate of photosynthesis based on gas exchange measurements and the thylakoid electron flux based on chlorophyll fluorescence were used to investigate physiological limitations to photosynthesis in leaves of deficit irrigated tomato plants under open field situations. Combined leaf gas exchange/chlorophyll fluorescence measurements differentiated the treatments effectively. Reduction in rate of photosynthesis, stomatal conductance and the maximum quantum efficiency of photosystem II varied across seasons of all varieties, whereas leaf temperature was increased by deficit irrigation in all varieties. Among varieties studied, Miya was found relatively tolerant to deficit irrigation. Stomatal limitation of rate of photosynthesis increased significantly as a result of water stress suggesting a strong influence of the stomatal behaviour. We also determined the influence of irrigation systems and strategies on water saving and tomato fruit quality. Using deficit drip irrigation was the best management strategy to optimize water use and tomato quality. Fruit dry matter content, acid content and total soluble solids were significantly higher with deficit drip irrigation than with other treatments. From this thesis it appeared that agro-climatic conditions, access to resources and culture all contribute to the relatively low yields of tomato in the Central Rift Valley of Ethiopia. The thesis also proved that significant advances can be made in yield, quality and resource use efficiency.

Drought stress and sub-optimal soil fertility management are major constraints to crop production in general and to cassava (Manihot esculenta Crantz) in particular in the rain-fed cropping systems in West Africa. Cassava is an important source of calories for millions of smallholder households in sub-Sahara Africa. The prime aim of this research was to understand cassava productivity in order to contribute to improving yields, food security and farm incomes in rain-fed cassava production systems in West Africa. A long-term goal was to contribute to a decision support tool for site-specific crop and nutrient management recommendations. Firstly, we studied farmers’ perception of cassava production constraints, assessed drivers of diversity among households and analysed the suitability of farmers’ resource endowment groups to the intensification of cassava production. The results indicate that farmers perceived erratic rainfall and poor soil fertility to be prime constraints to cassava production. The agricultural potential of the area and the proximity to regional markets were major drivers for the adoption of crop intensification options including the use of mineral and organic fertilizers. While the use of mineral and organic fertilizers was common in the Maritime zone that had a low agricultural potential, storage roots yields were below the national average of 2.2 Mg dry matter per hectare, and average incomes of 0.62, 0.46 and 0.46 US$ per capita per day for the high, medium and low farmer resource groups (REGs – HRE, MRE and LRE, respectively) were below the poverty line requirement of 1.25 US$. In the high agricultural potential Plateaux zone, HRE and MRE households passed this poverty line by earning 2.58 and 2.59 US$ per capita per day, respectively, unlike the LRE households with 0.89 US$ per capita per day. Secondly, we investigated the effects of mineral fertilizer on nutrient uptake, nutrient physiological use efficiency and storage roots yields of cassava since soil fertility was a major issue across the zones. We used an approach based on the model for the Quantitative Evaluation of the Fertility of Tropical Soils (QUEFTS). This model was successfully adapted for cassava and it appropriately assessed the response of cassava to N, P and K applications, especially in years with good rainfall. Under high drought stress, the model overestimated cassava yields. Thirdly, we investigated the impact of balanced nutrition on nutrient use efficiency, yield and return on investment compared to blanket fertilizer use as commonly practiced in cassava production systems in Southern Togo, and in Southern and Northern Ghana. The balanced nutrition approach of the QUEFTS model aimed to maximize simultaneously nutrient use efficiency of N, P and K in accordance with the plant’s needs. Larger nutrient use efficiencies of 20.5 to 23.9 kg storage root dry matter (DM) per kilo crop nutrient equivalent (1kCNE of a nutrient is the quantity of that nutrient that has the same effect on yield as 1 kg of N under balanced nutrition conditions) were achieved at balanced nutrition at harvest index (HI) of 0.50 compared to 20.0 to 20.5 kg storage root DM per kilo CNE for the blanket rates recommended by national research services for cassava production. Lower benefit:cost ratios of 2.4±0.9 were obtained for the blanket fertilizer rates versus 3.8±1.1 for the balanced fertilizer rates. Our study revealed that potassium (K) was a major yield limiting factor for cassava production, especially on the Ferralsols in Southern Togo. Hence, we fourthly studied the effect of K and its interaction with nitrogen (N), phosphorus (P), and the timing of harvest on the productivity of cassava in relation to the effects of K on radiation use efficiency (RUE), light interception, water use efficiency (WUE) and water transpiration. The results suggest that K plays a leading role in RUE and WUE, while N is the leading nutrient for light interception and water transpiration. Potassium effects on RUE and WUE depended on the availability of N and harvest time. Values of RUE and WUE declined with harvest at 4, 8 and 11 months after planting. Thus, enhanced K management with sufficient supply of N during the early stage of development of cassava is needed to maximize RUE and WUE, and consequently attain larger storage root yields. Given that erratic rainfall was another major constraint to cassava production according to the results of the farm survey, and due to the inability of QUEFTS modelling to assess drought effects on cassava yield successfully, another modelling approach based on light interception and utilization (LINTUL) was used. We quantified drought impacts on yields and explored strategies to improve yields through evaluation of planting dates in Southern Togo. The evaluation of the model indicated good agreement between simulated and observed leaf area index (Normalised Root Mean Square Error - NRMSE - 17% of the average observed LAI), storage roots yields (NRMSE 5.8% of the average observed yield) and total biomass yield (NRMSE 5.8% of the average observed). Simulated yield losses due to drought ranged from 9-60% of the water-limited yields. The evaluation of planting dates from mid-January to mid-July indicated that the best planting window is around mid-February. Higher amount of cropping season rainfall was also achieved with early planting. These results contradict current practices of starting planting around mid-March to mid-April. However, the results indicate the possibility to increase cassava yields with early planting, which led to less yield losses due to drought. By contrast, late planting around June-July gave larger potential yields, and suggested these periods to be the best planting window for cassava under irrigated conditions in Southern Togo. This shows that appropriate water control and planting periods can contribute to attaining larger yields in Southern Togo. Further improvement of the LINTUL model is required towards using it to assess water-limited yield, which can be used as boundary constraint in QUEFTS to derive site-specific fertilizer requirements for enhanced cassava yield and returns on investments in West Africa.

The aim of this thesis was to improve understanding of the role of organic inputs and soil organic matter (SOM) for crop production in contemporary arable farming in Europe. For this purpose, long-term experiments were analysed on the additional yield effect of organic inputs and savings in mineral fertiliser. In addition, a farm survey was conducted to find drivers and barriers for the use of organic inputs and to assess if arable farmers in Europe perceive a deficiency of SOM. The findings in this thesis suggest that at least on the shorter term, on average, there seems to be no immediate threat from a deficiency of SOM to crop production in arable farming in Europe. The long-term experiments showed that with sufficient use of only mineral fertilisers, on average, similar yields could be attained over multiple years as with the combined use of organic inputs and mineral fertiliser. This was reflected in the farm survey, in which a large majority of farmers indicated not to perceive a deficiency of SOM. Analysis of long-term experiments also showed that more mineral fertiliser N was saved when using farmyard manure at high N rates (with mineral fertiliser application) than at low N rates (without mineral fertiliser application), based on comparisons at equal yield. Specific crops and environments did benefit from organic inputs and more SOM in terms of crop production. Long-term experiments showed that organic inputs give benefit to crop production in wet climates and on sandy soils. In addition, farmers perceived a higher deficiency of SOM on steep slopes, sandy soils, wet and very dry climates. The additional yield effect of organic inputs was significant for potatoes. More in general, farmers who cultivated larger shares of their land with specialized crops (including potatoes, sugar beets, onions and other vegetables) than cereals perceived a higher deficiency of SOM. It seems that while the functions of SOM can be replaced with technical means to a large extent (e.g. tillage, use of mineral fertilisers), there are limits to this technical potential when environmental conditions are more extreme and crops are more demanding. The farm survey revealed that farmers perceive a trade-off between improved soil quality on the one hand and increased pressures from weeds, pests and diseases and financial consequences on the other hand when using organic inputs. If policies aim to stimulate the maintenance or increase of SOM, more insight is needed into the conditions that regulate the pressures of weeds, pests and diseases in response to organic inputs. Financial consequences (at least on the short term) should also be accounted for. More importantly however, benefits from SOM for crop production cannot be taken for granted. Only in specific situations such benefits will exist. If European policies on SOM aim to include benefits for crop production, focus should be on areas with more extreme environmental conditions (very dry or wet climates, steep slopes, sandy soils), or cropping systems with more specialized or horticultural crops rather than cereals.

The performance of publicly funded canal irrigation systems or more commonly called national irrigation systems (NIS) in the Philippines remained below expectations despite considerable system rehabilitation and improvement efforts. The continued suboptimal performances were attributed to technical, managerial, institutional and policy issues and constraints, and in recent years, to climate change. Irrigation modernisation is recognized as strategic option to improve the irrigation system performance. It is defined as a process of technical, management and institutional transformation to improve irrigation services to farmers. The main objective of the research study was to formulate a strategy for developing a modernisation plan for national irrigation systems in the Philippines. The research methodology was framed with deliberately selected assessment and characterization procedures, which were adoptively modified and integrated to critically analyse the state of coherence among the three fundamentals of irrigation system water delivery: design, operation and water supply; and to identify solutions for any inconsistency. It included, among others an analysis of the process, nature and impacts of rehabilitation projects; diagnostic assessment of the irrigation systems; revalidation of design assumptions on water balance parameters; characterization of irrigation management, service and demands; and identification of options for improvements. The developed methodology for examining the different aspects of planning and operations of NIS with an end view of modernising the systems provides a more comprehensive and applicable methodology for drawing up of a more relevant plan for NIS modernisation. The knowledge gained on case study systems provides a sound basis for planning of appropriate modernisation solutions for the case study systems and in cases of ungauged, small-scale NIS. The methodology developed in this study could serve as a blueprint for modernisation program for NIS.

Over the last decades agricultural production increased drastically due to the use of external inputs. However, the use of external inputs has high environmental costs and may negatively influence ecosystem processes such as pollination and pest control that underpin agricultural production. Soil organic matter has been proposed as a potential alternative to external inputs as it relates to multiple yield promoting ecosystem processes. The aim of my thesis is to assess whether and how soil organic matter content alters the effect of some ecosystem processes and external inputs on crop yield. I examined whether soil organic matter alters biomass of wheat and oilseed rape under fertilizer supply. Other biotic and abiotic factors that operate at different spatial and temporal scales are also included in some of these experiments. I found that under controlled conditions soil organic matter may reduce the positive effect of mineral fertilizer supply on crop biomass. The reduction changed with the presence or absence of a pathogenic root fungus, but not with drought stress. Moreover, soil organic matter enhances performance of aphids under controlled greenhouse conditions, but the enhancement was less than fertilizer supply. None of these controlled experiments, however, showed that soil organic matter can be an alternative to mineral fertilizer supply. Under field conditions soil organic matter did not strongly affect plant nutrient availability or performances of aphid and its natural enemies. The relation between soil organic matter and plant biomass in a greenhouse experiment did not change with organic management or the duration of it, neither did it change with pollinator visitation rate, an ecosystem process that is managed on the landscape scale. These results suggest that soil organic matter may relate to ecosystem services that influence crop yield, whereas these relations might not be significant under field conditions. Collectively, all these results suggest that the relation between soil organic matter content and ecosystem processes that benefit crop yield is highly context dependent. I propose future research may focus on (1) the quality of soil organic matter rather than the content per se and (2) the relation between soil organic matter content and crop yield under realistic conditions in a longer term.

The world population is anticipated to be around 9.1 billion in 2050 and the challenge is how to feed this huge number of people without affecting natural ecosystems. Different approaches have been proposed and closing the ‘yield gap’ on currently available agricultural lands is one of them. The concept of ‘yield gap’ is based on production ecological principles and can be estimated as the difference between a benchmark (e.g. climatic potential or water-limited yield) and the actual yield. Yield gap analysis can be performed at different scales: from field to global level. Of particular importance is estimating the yield gap and revealing the underlying explanatory factors contributing to it. As decisions are made by farmers, farm level yield gap analysis specifically contributes to better understanding, and provides entry points to increased production levels in specific farming systems. A major challenge for this type of analysis is the high data standards required which typically refer to (a) large sample size, (b) fine resolution and (c) great level of detail. Clearly, obtaining information about biophysical characteristics and crop and farm management for individual agricultural activities within a farm, as well as farm and farmer’s characteristics and socio-economic conditions for a large number of farms is costly and time-consuming. Nowadays, the proliferation of different types of mobile phones (e.g., smartphones) equipped with sensors (e.g., GPS, camera) makes it possible to implement effective and low-cost “bottom-up” data collection approaches such as citizen science. Using these innovative methodologies facilitate the collection of relatively large amounts of information directly from local communities. Moreover, other data collection methods such as remote sensing can provide data (e.g., on actual crop yield) for yield gap analysis. The main objective of this thesis, therefore, was to investigate the applicability of innovative data collection approaches such as crowdsourcing and remote sensing to support the assessment and monitoring of crop yield gaps. To address the main objective, the following research questions were formulated: 1) What are the main factors causing the yield gaps at the global, regional and crop level? 2) How could data for yield gap explaining factors be collected with innovative “bottom-up” approaches? 3) What are motivations of farmers to participate in agricultural citizen science? 4) What determines smallholder farmers to use technologies (e.g., mobile SMS) for agricultural data collection? 5) How can synergy of crowdsourced data and remote sensing improve the estimation and explanation of yield variability? Chapter 2 assesses data availability and data collection approaches for yield gap analysis and provides a summary of yield gap explaining factors at the global, regional and crop level, identified by previous studies. For this purpose, a review of yield gap studies (50 agronomic-based peer-reviewed articles) was performed to identify the most commonly considered and explaining factors of the yield gap. Using the review, we show that management and edaphic factors are more often considered to explain the yield gap compared to farm(er) characteristics and socio-economic factors. However, when considered, both farm(er) characteristics and socio-economic factors often explain the yield gap. Furthermore, within group comparison shows that fertilization and soil fertility factors are the most often considered management and edaphic groups. In the fertilization group, factors related to quantity (e.g., N fertilizer quantity) are more often considered compared to factors related to timing (e.g., N fertilizer timing). However, when considered, timing explained the yield gap more often. Finally, from the results at regional and crop level, it was evident that the relevance of factors depends on the location and crop, and that generalizations should not be made. Although the data included in yield gap analysis also depends on the objective, knowledge of explaining factors, and methods applied, data availability is a major limiting factor. Therefore, bottom-up data collection approaches (e.g., crowdsourcing) involving agricultural communities can provide alternatives to overcome this limitation and improve yield gap analysis. Chapter 3 explores the motivations of farmers to participate in citizen science. Building on motivational factors identified from previous citizen science studies, a questionnaire based methodology was developed which allowed the analysis of motivational factors and their relation to farmers’ characteristics. Using the developed questionnaire, semi-structured interviews were conducted with smallholder farmers in three countries (Ethiopia, Honduras and India). The results show that for Indian farmers a collectivistic type of motivation (i.e., contribute to scientific research) was more important than egoistic and altruistic motivations. For Ethiopian and Honduran farmers an egoistic intrinsic type of motivation (i.e., interest in sharing information) was most important. Moreover, the majority of the farmers in the three countries indicated that they would like to receive agronomic advice, capacity building and seed innovation as the main returns from the citizen science process. Country and education level were the two most important farmers’ characteristics that explained around 20% of the variation in farmers’ motivations. The results also show that motivations to participate in citizen science are different for smallholders in agriculture compared to other sectors. For example fun has appeared to be an important egoistic intrinsic factor to participate in other citizen science projects, the smallholder farmers involved in this research valued ‘passing free time’ the lowest. Chapter 4 investigates the factors that determine farmers to adopt mobile technology for agricultural data collection. To identify the factors, the unified theory of acceptance and use of technology (UTAUT2) model was employed and extended with additional constructs of trust, mastery-approach goals and personal innovativeness in information technology. As part of the research, we setup data collection platforms using open source applications (Frontline SMS and Ushahidi) and farmers provided their farm related information using SMS for two growing seasons. The sample for this research consisted of group of farmers involved in a mobile SMS experiment (n=110) and another group of farmers which was not involved in a mobile SMS experiment (n=110), in three regions of Ethiopia. The results from the structural equation modelling showed that performance expectancy, effort expectancy, price value and trust were the main factors that influence farmers to adopt mobile SMS technology for agricultural data collection. Among these factors, trust is the strongest predictor of farmer’s intention to adopt mobile SMS. This clearly indicates that in order to use the citizen science approach in the agricultural domain, establishing a trusted relationship with the smallholder farming community is crucial. Given that performance expectancy significantly predicted farmer’s behavioural intention to adopt mobile SMS, managers of agricultural citizen science projects need to ensure that using mobile SMS for agricultural data collection offers utilitarian benefits to the farmers. The importance of effort expectancy on farmer’s intention to adopt mobile SMS clearly indicates that mobile phone software developers need to develop easy to use mobile applications. Chapter 5 demonstrates the results of synergetic use of remote sensing and crowdsourcing for estimating and explaining crop yields at the field level. Sesame production on medium and large farms in Ethiopia was used as a case study. To evaluate the added value of the crowdsourcing approach to improve the prediction of sesame yield using remote sensing, two independent models based on the relationship between vegetation indices (VIs) and farmers reported yield were developed and compared. The first model was based on VI values extracted from all available remote sensing imagery acquired during the optimum growing period (hereafter optimum growing period VI). The second model was based on VI values extracted from remote sensing imagery acquired after sowing and before harvest dates per field (hereafter phenologically adjusted VI). To select the images acquired between sowing and harvesting dates per field, farmers crowdsourced crop phenology information was used. Results showed that vegetation indices derived based on farmers crowdsourced crop phenology information had a stronger relationship with sesame yield compared to vegetation indices derived based on the optimum growing period. This implies that using crowdsourced information related to crop phenology per field used to adjust the VIs, improved the performance of the model to predict sesame yield. Crowdsourcing was further used to identify the factors causing the yield variability within a field. According to the perception of farmers, overall soil fertility was the most important factor explaining the yield variability within a field, followed by high presence of weeds. Chapter 6 discusses the main findings of this thesis. It draws conclusions about the main research findings in each of the research questions addressed in the four main chapters. Finally, it discusses the necessary additional steps (e.g., data quality, sustainability) in a broader context that need to be considered to utilize the full potential of innovative data collection approaches for agricultural citizen science.

Yield gap analysis is useful to understand the relative contribution of growth-defining, -limiting and -reducing factors to actual yields. This is traditionally performed at the field level using mechanistic crop growth simulation models, and directly up-scaled to the regional and global levels without considering a range of factors intersecting at farm and farming system levels. As an example, these may include farmers' objectives and resource constraints, farm(er) characteristics, rotational effects between subsequent crops or decisions on resource allocation and prioritization of crop management. The objective of this thesis is to gain insights into yield gaps from a farm(ing) systems perspective in order to identify opportunities for sustainable intensification at local level. Three contrasting case studies representing a gradient of intensification and capturing a diversity of agricultural systems were selected for this purpose, namely mixed crop-livestock systems in Southern Ethiopia, rice based-farming systems in Central Luzon (Philippines) and arable farming systems in the Netherlands. A theoretical framework combining concepts of production ecology and methods of frontier analysis was developed to decompose yield gaps into efficiency, resource and technology yield gaps. This framework was applied and tested for the major crops in each case study using crop-specific input-output data for a large number of individual farms. In addition, different statistical methods and data analyses techniques were used in each case study to understand the contribution of farmers' objectives, farm(er) characteristics, cropping frequency and resource constraints to yield gaps and management practices at crop level. Yield gaps were largest for maize and wheat in Southern Ethiopia (ca. 80\\% of the water-limited yield), intermediate for rice in Central Luzon (ca. 50\\% of the climatic potential yield) and smallest for the major arable crops in the Netherlands (ca. 30\\% of the climatic potential yield). The underlying causes of these yield gaps also differed per case study. The technology yield gap explained most of the yield gap observed in Southern Ethiopia, which points to a lack of adoption of technologies able to reach the water-limited yield. The efficiency yield gap was most important for different arable crops in the Netherlands, which suggests a sub-optimal timing, space and form of the inputs applied. The three intermediate yield gaps contributed similarly to the rice yield gap in Central Luzon meaning that sub-optimal quantities of inputs used are as important in this case study as the causes mentioned for the other case studies. Narrowing the yield gap of the major crops does not seem to entail trade-offs with gross margin per unit land in each case study. However, the opposite seems to be true for N use efficiency and labour productivity particularly in Southern Ethiopia and Central Luzon, and to a less extent in the Netherlands. This means that (sustainable) intensification of smallholder agriculture in the tropics needs to go hand-in-hand with agronomic interventions that increase land productivity while ensuring high resource use efficiency and with labour-saving technologies that can reduce the drudgery of farming without compromising crop yields. Other insights at farm(ing) system level were clearer in Southern Ethiopia than in Central Luzon or in the Netherlands. For example, alleviating capital constraints was positively associated with intensification of maize-based farming systems around Hawassa and increases in oxen ownership (an indicator of farm power) was associated with extensification of wheat-based farming systems around Asella. In Central Luzon, farm and regional factors did not lead to different levels of intensification within the variation of rice farms investigated and the most striking effect was that direct-seeding (and thus slightly lower rice yields) was mostly adopted in larger farms, and used lower amounts of hired labour, compared to transplanting. In the Netherlands, the analysis of rotational effects on crop yields provided inconclusive results but confounding effects with e.g. rented land do not allow to conclude that these are not at stake in this farming system. This thesis broadens the discussion on yield gaps by moving from the technical aspects underlying their estimation towards the broader farm level opportunities and constraints undermining their closure. Overall, insights from contrasting case studies support conventional wisdom that intensification of agriculture needs to occur in the 'developing South', where yield gaps are large and resource use efficiency low, while a focus on improving sustainability based on sustainable intensification (or even extensification) is more appropriate in the 'developed North', where yield gaps are small and resource use efficiency high.

A plurality of components (such as sugars, lignin, pectin) of Miscanthus x giganteus has been studied in stem, leaf, and rhizomes for the harvest times July and January in view of the optimal harvest time. Additional literature search shows that the end of October is the optimum time for harvesting on the basis of the maximum above-ground dry matter yield and sugar yield, and dry matter yield in the next year. It will have to be investigated whether the optimal harvest time also applies to long-term research. Een aantal inhoudsstoffen (o.a. suikers, lignine, pectine) van Miscanthus x giganteus is onderzocht in stengel, blad en rhizomen voor de oogstmomenten juli en januari met het oog op het optimale oogstmoment. Aanvullend literatuuronderzoek toont aan dat eind oktober het optimale oogstmoment is op basis van maximale bovengrondse drogestof- en suikeropbrengst en drogestofopbrengst in het volgende jaar. Nagegaan zal moeten worden of dit optimale oogstmoment ook geldt bij langjarig onderzoek.

Recente studies van onder meer IPCC1 en de Wereldbank2 voorspellen rampzalige gevolgen voor de wereldvoedselvoorziening als gevolg van klimaatverandering. Afgezien van lokaal optredende effecten, zoals permanent ondergelopen akkers of temperaturen die te hoog zijn voor bloei en zaadzetting, is het effect van klimaatverandering op de productie van gewassen vooral relatief, meent Maja Slingerland. Veel belangrijker is het om de yield gap, het gat tussen feitelijke en potentiële opbrengst per hectare, te dichten.

The Central Rift Valley (CRV) of Ethiopia is a closed basin for which claims on land and water have strongly increased over the past decade resulting in over-exploitation of the resources. A clear symptom is the declining trend in the water level of the terminal Lake Abyata. The actual productivity of most cereals in the CRV is less than 2 t ha-1 associated with low input use and poor crop management. Consequently, there are two major development objectives in the CRV, i.e. producing sufficient food for the increasing population, while at the same time ensuring efficient use of limited water and land resources under variable and changing climate conditions. The low productive cereal systems and a declining resource base call for options to increase crop productivity and improve resource use efficiency in order to meet the growing demand for food. In this thesis, the recent impacts were quantified of climate change, land use change and irrigation water abstraction on water availability of Lake Abyata of the CRV. The trends in lake levels, river discharges, basin rainfall, temperature and irrigation development (ca. 1975-2008) were analysed and the additional evapotranspiration loss resulting from temperature change and irrigated land were computed. We also analysed land use change (1990-2007) and the associated changes in runoff. Results showed that temperature has increased over 34 years (p10,000) and experimental data across the CRV from 2004-2009 to quantify the gaps (Yg) between actual (farm) and experimental (water-limited potential - Yw) yields of maize and wheat in homogenous farming zones. We found that the average (2004-2009) yield gap of maize and wheat ranged between 4.2-9.2 t ha-1, and 2.5-4.7 t ha-1, respectively, across farming zones. The actual N and P application in farmers’ fields was low, as about 46% of maize and 27% of wheat fields did not receive fertilisers. We calibrated, validated and used the Agricultural Production System Simulator (APSIM) model to explore intensification options and their trade-offs with water losses through evapotranspiration. Variety selection and N fertilization were more important for yield gap closure than crop residue management and planting density, and the magnitude of their effect depended on soil type and climate. There was a trade-off between intensification and water use through evapotranspiration, as increasing yield comes at the cost of increased transpiration. However, this trade-off can be minimized by choosing location-specific N levels at which both water use efficiency (WUE) and gross margin are maximised. These application rates varied between 75 and 250 kg N ha-1 across locations and soils, and allowed producing 80% of Yw of maize and wheat. Climate change was projected to lower Yw of maize and wheat by ca. 15-25% and 2-30%, respectively, compared to current climate conditions. An automated gridded simulation framework was developed to scale up the promising intensification options from field scale to basin scale. We then aggregated basin scale production and identified trade-offs between production and water use for different land use scenarios. This procedure allowed designing land use scenarios based on a spatially explicit optimization of WUE and gross margin per grid cell. Consequences of land use scenarios for food production and water use at basin level were evaluated. Results of the different land use scenarios demonstrated that crop intensification options for which WUE and gross margin are maximised can meet the projected food demand (year 2050) of the growing population in the CRV while at the same time saving large areas of the currently cultivated land. In the intensification scenarios total water loss through evapotranspiration from agricultural land is reduced compared with water loss from current cultivated land and low crop productivity levels. It is concluded that the current land use together with climate change and water abstraction for irrigation negatively affected the basin level water balance in CRV over the past decade. Furthermore, the scope for further expansion of farmland to increase food production is very limited. The focus should, therefore, be towards intensification also because the existing yield gaps are huge and hence the scope for intensification is large. Model-based exploration of intensification options can be used to prioritize promising options, to close the yield gap and for quantifying trade-offs. Scaling up of promising options allows to assess whether the food demand of the growing population can be met while at the same time saving the less productive land and water per unit agricultural product.

Croplands are a managed type of vegetation, with a carbon storage that is highly optimized for food production. For instance, their sowing dates are chosen by the farmers, their genetic potential is bred for high grain yields, and their on-field competition with other species is reduced to the minimum. As a result of human intervention, croplands are a major land cover type (roughly one fifth of the land area over Europe) and they experience a short growing season during which they exchange carbon and water intensively with the atmosphere. Their growth significantly affects the seasonal amplitude of CO2 mole fractions over the globe, interact with extreme weather events such as droughts and heat waves, and impact surface hydrology due to their water consumption. However, and in spite of their relevance, terrestrial biosphere models used in carbon cycle and atmospheric research often assume the phenology of croplands to be similar to the one of grasslands, and they also ignore the impact of crop management. This oversimplification is the motivation for this thesis. We focus on understanding and modeling the key surface and atmospheric processes that shape the cropland water and CO2 exchange, and the resulting impact on the CO2 mole fractions of the atmosphere overhead. We study these processes from the daily to the seasonal scale, for croplands of the mid-latitudes. In the end, we come with recommendations and a new modeling framework to represent the cropland CO2 and water exchange in the Earth System, weather and climate models.

In dit onderzoek zijn 9 agrarische melkveebedrijven in Drenthe bezocht en is samen met de betrokken agrariers besproken en geanalyseerd in hoeverre de situatie op het erf en de percelen verbeterd kan worden ten aanzien van bodem en water. Vanuit gesignaleerde knelpunten zijn maatregelen aangedragen die bij kunnen dragen aan verbetering van het bedrijfsresultaat en het watersysteem. Samen met het waterschap zijn een 6-tal type maatregelen geselecteerd waarvan de effectiviteit is berekend. Hierbij is gebruik gemaakt van modellen die op perceelsniveau de vochthuishouding, gewasopbrengst en nutrientenhuishouding simuleren. Voor ieder bedrijf zijn de resultaten van het veldbezoek, analyse en berekening van effecten opgenomen in een bedrijfswaterplan, welke voor feedback is voorgelegd aan de betreffende agrarier. Het voorliggende rapport vat de resultaten van de 9 bedrijfswaterplannen samen en geeft op hoofdlijnen aan wat de potenties zijn van maatregelen op regionaal niveau.

Intercropping, the cultivation of two or more crop species simultaneously in the same field, has been widely practiced by smallholder farmers in developing countries and is gaining increasing interest in developed countries. Intercropping can increase the yield per unit land compared to sole cropping. The yield advantage of intercropping is often assessed using the land equivalent ratio (LER). LER may be interpreted as the relative area required by sole crops to produce the same yields as achieved in a unit area of intercrop. LER>1 means intercropping is more efficient in land use than sole cropping. A large variation of LER has been found in the literature. However, few studies attempted to investigate reasons for this variation in LER. This thesis aims to reveal how temporal niche difference, crop type combination, and agronomic practices affect LER, productivity and interspecific interactions in annual intercrops. LER increased with temporal niche differentiation according to our meta-analysis of literature data. This positive relationship was valid in mixtures of C3 and C4 species but not in C3/C3 mixtures. Application of N fertilizer in intercropping decreased LER when the intercropped species were sown and harvested simultaneously. However, reducing overlap in growing periods of the intercropped species mitigated the negative effect of N fertilizer on LER. A functional-structural plant (FSP) model was developed to investigate the interplay between temporal and spatial complementarity and plant traits in mixed plant systems. The results showed that complementarity of light use in time and space likely determine productivity of species mixtures. The early-sown plants benefited from later sowing of the late-sown plants due to the relaxed competition for light from the late-sown plants until a plateau when the growth durations of the intercropped species overlapped less than 50% of the total growth period of the intercrop. By contrast, the late-sown plants suffered a great reduction in biomass due to the competition for light from the early-sown plants especially at moderately delayed sowing time and when spatial arrangement of the intercrop allowed strong interspecific competition. The shading effect from the early-sown plants on the growth and productivity of the late-sown plants was smaller if the late-sown plants had the potential to grow tall and if it had a high maximum CO2 assimilation rate. A meta-analysis of relative yields in cereal/legume intercrops was conducted to investigate the relationship between performance of intercropped species and management. Earlier sowing of one species increased its competitiveness towards the other species while later sowing decreased it. Application of N fertilizer enhanced the competitiveness of a cereal towards a legume, resulting in overall low productivity of legumes in intercrops. However, sowing legumes earlier than cereals mitigated the negative effect of N on productivity of legumes. Overall, this thesis shows that the complementary resource use resulting from plant traits diversity and temporal and spatial arrangements of plant mixtures is one of the key factors for high productivity of intercropping. This finding strengthens the basis for further research on the possible contribution of species diversity in agricultural systems to meeting the demand for food and other agricultural products while mitigating the environmental impacts of modern agriculture.

Sinds 2013 zoekt Koeien & Kansen naar mogelijkheden om de ruwvoerproductie te verbeteren onder het motto ‘Naar een productieslag voor ruwvoer’. De aanpak is doelgericht: evalueren van de bestaande ruwvoerproductie om toe te werken naar een haalbaar geachte, hogere productie. In dit artikel gaan we in op het proces en geven we een ‘door de oogharen beeld’ van resultaten.

Intercropping, the cultivation of two or more crop species simultaneously in the same field, has been widely practiced by smallholder farmers in developing countries and is gaining increasing interest in developed countries. Intercropping can increase the yield per unit land compared to sole cropping. The yield advantage of intercropping is often assessed using the land equivalent ratio (LER). LER may be interpreted as the relative area required by sole crops to produce the same yields as achieved in a unit area of intercrop. LER>1 means intercropping is more efficient in land use than sole cropping. A large variation of LER has been found in the literature. However, few studies attempted to investigate reasons for this variation in LER. This thesis aims to reveal how temporal niche difference, crop type combination, and agronomic practices affect LER, productivity and interspecific interactions in annual intercrops. LER increased with temporal niche differentiation according to our meta-analysis of literature data. This positive relationship was valid in mixtures of C3 and C4 species but not in C3/C3 mixtures. Application of N fertilizer in intercropping decreased LER when the intercropped species were sown and harvested simultaneously. However, reducing overlap in growing periods of the intercropped species mitigated the negative effect of N fertilizer on LER. A functional-structural plant (FSP) model was developed to investigate the interplay between temporal and spatial complementarity and plant traits in mixed plant systems. The results showed that complementarity of light use in time and space likely determine productivity of species mixtures. The early-sown plants benefited from later sowing of the late-sown plants due to the relaxed competition for light from the late-sown plants until a plateau when the growth durations of the intercropped species overlapped less than 50% of the total growth period of the intercrop. By contrast, the late-sown plants suffered a great reduction in biomass due to the competition for light from the early-sown plants especially at moderately delayed sowing time and when spatial arrangement of the intercrop allowed strong interspecific competition. The shading effect from the early-sown plants on the growth and productivity of the late-sown plants was smaller if the late-sown plants had the potential to grow tall and if it had a high maximum CO2 assimilation rate. A meta-analysis of relative yields in cereal/legume intercrops was conducted to investigate the relationship between performance of intercropped species and management. Earlier sowing of one species increased its competitiveness towards the other species while later sowing decreased it. Application of N fertilizer enhanced the competitiveness of a cereal towards a legume, resulting in overall low productivity of legumes in intercrops. However, sowing legumes earlier than cereals mitigated the negative effect of N on productivity of legumes. Overall, this thesis shows that the complementary resource use resulting from plant traits diversity and temporal and spatial arrangements of plant mixtures is one of the key factors for high productivity of intercropping. This finding strengthens the basis for further research on the possible contribution of species diversity in agricultural systems to meeting the demand for food and other agricultural products while mitigating the environmental impacts of modern agriculture.

Vanwege de eindigheid van de wereldvoorraad makkelijk winbaar fossiel fosfor en om fosforemissies uit (overbemeste) landbouwgronden naar grond- en oppervlaktewater te verminderen, is het Nederlandse landbouwbeleid gericht op het verlagen van fosforbemesting. Het doel van dit beleid is om de P-toestand in bodems met een hoge fosfortoestand te laten dalen en relatief lage toestanden in bodems niet meer dan landbouwkundig noodzakelijk te verhogen. Op termijn speelt de vraag hoe bij lage fosforbemesting toch nog goed gewassen te telen zijn. Het wordt steeds belangrijker om het fosfor dat in de bodem aanwezig is, te benutten. Binnen project Verbetering benutting bodemvoorraad fosfaat wordt onderzocht hoe dit kan en of dit gekwantificeerd kan worden. Het project wordt uitgevoerd door het Louis Bolk Instituut en PPOAGV.

In this thesis we describe the results of a number of quantitative techniques that were used to understand the genetics of yield in pepper as an example of complex trait measured in a number of environments. Main objectives were; i) to propose a number of mixed models to detect QTLs for multiple traits and multiple environments, ii) to extend the multi-trait QTL models to a multi-trait genomic prediction model, iii) to study how well the complex trait yield can be indirectly predicted from its component traits, and iv) to understand the ‘causal’ relationships between the target trait yield and its component traits. The thesis is part of an EU-FP7 project “ S mart tools for P rediction and I mprovements of C rop Y ield” (SPICY- http://www.spicyweb.eu/). This project generated phenotypic data from four environments using 149 individuals from the sixth generation of recombinant inbred lines obtained from intraspecific cross between large – fruited inbred pepper cultivar ‘Yolo Wonder’ (YW) and the hot pepper cultivar ‘Criollo de Morelos 334’ (CM 334). A total of 16 physiological traits were evaluated across the four trials and various types of genetic parameters were estimated. In a first analysis, the traits were univariately analyzed using linear mixed model. Trait heritabilities were generally large (ranging between 0.43 – 0.96 with an average of 0.86) and mostly comparable across trials while many of the traits displayed heterosis and transgression. The same QTLs were detected across the four trials, though QTL magnitude differed for many of the traits. We also found that some QTLs affected more than one trait, suggesting QTL pleiotropy (a QTL region affecting more than one trait). We discussed our results in the light of previously reported QTLs for these and similar traits in pepper. We addressed the presence of genotype-by-environment interaction (GEI) in yield and the other traits through a multi-environment (ME) mixed model methodology with terms for QTL-by-environment interaction (QEI). We opined that yield would benefit from joint analysis with other traits and so deployed two other mixed model based multi-response QTL approaches: a multi-trait approach (MT) and a multi-trait multi-environment approach (MTME). For yield as well as the other traits, MTME was superior to ME and MT in the number of QTLs, the explained variance and accuracy of predictions. Many of the detected QTLs were pleiotropic and showed quantitative QEI. The results confirmed the feasibility and strengths of novel mixed model QTL methodology to study the architecture of complex traits. The QTL methods considered thus far are not well suited for prediction purposes as only a limited set of QTL-related markers are used. Since the main interest of this research includes improvement of yield prediction, we explored both single-trait and multi-trait versions of genomic prediction (GP) models as alternatives to the QTL-based prediction (QP) models. This was termed direct prediction. The methods differed in their predictive accuracies with GP methods outperforming QP methods in both single and multi-traits situations. We borrowed ideas from crop growth model (CGM) to dissect complex trait yield into a number of its component traits. Here, we integrated QTL/genomic prediction and CGM approaches and showed that the target trait yield can be predicted via its component traits together with environmental covariables. This was termed indirect prediction. The CGM approach seemed to work well at first sight, but this is especially due to the fact that yield appeared to be strongly driven by just one of its components, the partitioning to fruit. An alternative representation of the biological knowledge of a complex target trait such as yield is provided by network type models. We constructed both conditional and unconditional networks across the four environments to understand the ‘causal’ relationships between target trait yield and its component traits. The final networks for each environment from both conditional and unconditional methods were used in a structural equation model to assess the causal relationships. Conditioning QTL mapping on network structure improved detection of refined genetic architecture by distinguishing between QTL with direct and indirect effects, thereby removing non-significant effects found in the unconditional network and resolving QTL pleiotropy. Similar to the CGM topology, yield was established to be downstream to its component traits, indicating that yield can be studied and predicted from its component traits. Thus, the genetic improvements of yield would benefit from improvements on the component traits. Finally, complex trait prediction can be enhanced by a full integration of the methods described in the different chapters. Recent research efforts have been channelled to incorporating both multivariate whole genome prediction models and crop growth models. Further research is required, but we hope that the present thesis presents useful steps towards better prediction models for complex traits exhibiting genotype by environment interaction.

Deze studie over Nederlandse bodemschimmels heeft geleidt tot een eerste exemplaar van een overzichtelijk schema met gewassen in relatie tot schadepotentieel en vermeerdering. Achtergrondinformatie over waardplanten, vermeerdering en schade is verzameld en beschreven van vijftien schimmels in 40 landbouwgewassen. Per ziekte is aangegeven op welke grondsoort deze (hoofdzakelijk) voorkomt en welke substantiële schade deze kan veroorzaken. Deze informatie biedt nieuwe mogelijkheden om beter te anticiperen op de grilligheid en incidentie van bodemgebonden schimmels. Het rapport vloeit voort uit de financiering door PT en PA.

Vanwege de eindigheid van de wereldvoorraad makkelijk winbaar fossiel fosfor en om fosforemissies uit (overbemeste) landbouwgronden naar grond- en oppervlaktewater te verminderen, is het Nederlandse landbouwbeleid gericht op het verlagen van fosforbemesting. Het doel van dit beleid is om de P-toestand in bodems met een hoge fosfortoestand te laten dalen en relatief lage toestanden in bodems niet meer dan landbouwkundig noodzakelijk te verhogen. Op termijn speelt de vraag hoe bij lage fosforbemesting toch nog goed gewassen te telen zijn. Het wordt steeds belangrijker om het fosfor dat in de bodem aanwezig is, te benutten. Binnen project Verbetering benutting bodemvoorraad fosfaat wordt onderzocht hoe dit kan en of dit gekwantificeerd kan worden. Het project wordt uitgevoerd door het Louis Bolk Instituut en PPOAGV.